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Yorodumi- PDB-6pj4: Time-resolved structural snapshot of proteolysis by GlpG inside t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pj4 | ||||||
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Title | Time-resolved structural snapshot of proteolysis by GlpG inside the membrane | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/INHIBITOR / inhibitor complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information maternal determination of dorsal/ventral axis, ovarian follicular epithelium, germ-line encoded / dorsal/ventral axis specification, ovarian follicular epithelium / anterior/posterior axis specification, follicular epithelium / determination of dorsal identity / chorion-containing eggshell pattern formation / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / oocyte dorsal/ventral axis specification / imaginal disc-derived wing vein specification / dorsal appendage formation ...maternal determination of dorsal/ventral axis, ovarian follicular epithelium, germ-line encoded / dorsal/ventral axis specification, ovarian follicular epithelium / anterior/posterior axis specification, follicular epithelium / determination of dorsal identity / chorion-containing eggshell pattern formation / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / oocyte dorsal/ventral axis specification / imaginal disc-derived wing vein specification / dorsal appendage formation / positive regulation of border follicle cell migration / rhomboid protease / anterior/posterior pattern specification / epidermal growth factor receptor binding / epidermal growth factor receptor signaling pathway / endopeptidase activity / receptor ligand activity / cell surface receptor signaling pathway / serine-type endopeptidase activity / proteolysis / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Urban, S. / Cho, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Authors: Cho, S. / Baker, R.P. / Ji, M. / Urban, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pj4.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pj4.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 6pj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/6pj4 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/6pj4 | HTTPS FTP |
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-Related structure data
Related structure data | 6pj5C 6pj7C 6pj8C 6pj9C 6pjaC 6pjpC 6pjqC 6pjrC 6pjuC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23800.133 Da / Num. of mol.: 1 / Mutation: Y205F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, APT88_21985, SK83_00858 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0J2E248, UniProt: P09391*PLUS, rhomboid protease |
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#2: Protein/peptide | Mass: 405.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P42287*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Na-acetate pH5.5, 3M NaCl, 5% Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→62.69 Å / Num. obs: 10112 / % possible obs: 99.9 % / Redundancy: 6.1 % / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 963 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→57.63 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.618 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.21
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.665 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→57.63 Å
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Refine LS restraints |
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